Contacts of the helix formed by residues 1340 - 1360 (chain J) in PDB entry 4XLN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY1340 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1335J LEU 3.3 4.9 + - - +
1336J LEU 4.0 11.6 + - - -
1338J ALA 3.9 0.2 - - - -
1339J LYS* 1.3 79.6 - - - +
1341J PRO* 1.3 75.2 - - - +
1342J GLU* 3.3 6.6 + - - -
1343J ALA* 3.6 4.8 + - - +
1344J VAL* 3.2 26.2 + - - +
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Residues in contact with PRO1341 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1336J LEU* 4.2 10.9 - - + +
1340J GLY* 1.3 83.3 - - - +
1342J GLU* 1.3 78.3 + - + +
1344J VAL* 3.2 10.3 - - + +
1345J GLU* 2.9 36.8 + - - +
1376J LEU* 4.2 19.7 - - + +
1419J PRO* 4.6 23.8 - - + -
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Residues in contact with GLU1342 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118J ILE* 5.5 11.7 - - + -
1340J GLY* 3.3 4.1 - - - -
1341J PRO* 1.3 95.8 - - + +
1343J ALA* 1.3 63.1 + - - +
1345J GLU* 3.2 17.6 + - - +
1346J ARG* 2.9 23.9 + - - +
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Residues in contact with ALA1343 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335J LEU* 3.9 7.4 - - + +
1339J LYS* 3.6 39.7 - - + -
1340J GLY 3.6 3.7 + - - +
1341J PRO 3.4 0.2 - - - -
1342J GLU* 1.3 80.0 + - - +
1344J VAL* 1.3 57.1 + - - +
1346J ARG* 2.9 29.9 + - - +
1347J TYR* 2.9 28.8 + - - +
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Residues in contact with VAL1344 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332J PRO 4.0 1.3 - - - +
1335J LEU* 3.6 16.4 - - + -
1336J LEU* 3.5 40.2 - - + +
1340J GLY 3.2 15.3 - - - +
1341J PRO* 3.2 9.6 + - + +
1342J GLU 3.1 0.2 - - - -
1343J ALA* 1.3 74.5 - - - +
1345J GLU* 1.3 68.0 + - - +
1347J TYR* 2.9 5.2 + - - +
1348J LEU* 2.9 42.6 + - + +
1376J LEU* 4.4 9.9 - - + -
1421J LEU* 3.6 26.5 - - + -
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Residues in contact with GLU1345 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118J ILE* 5.1 7.3 - - - +
1192J LEU* 3.4 46.9 - - + +
1341J PRO* 2.9 24.1 + - - +
1342J GLU* 3.5 17.0 - - - +
1344J VAL* 1.3 71.8 - - - +
1346J ARG* 1.3 64.6 + - - +
1348J LEU* 3.8 0.6 - - - +
1349J VAL* 3.0 31.8 + - - +
1372J VAL* 3.7 22.2 - - + -
1373J ARG* 5.0 1.6 - - - +
1376J LEU* 3.6 31.7 - - + +
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Residues in contact with ARG1346 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121J PRO* 6.0 8.5 - - - -
1335J LEU* 5.7 0.6 - - - +
1339J LYS* 3.6 24.9 - - - +
1342J GLU 2.9 12.4 + - - +
1343J ALA* 2.9 45.7 + - - +
1345J GLU* 1.3 76.9 - - - +
1347J TYR* 1.3 61.4 + - - +
1349J VAL* 4.0 2.8 - - - +
1350J ASP* 2.9 37.5 + - + +
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Residues in contact with TYR1347 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258J ARG* 3.0 22.5 + - - -
1262J LEU* 4.8 7.9 - - + -
1329J ALA* 3.8 2.6 - - - +
1330J ILE* 3.2 61.8 + - + +
1332J PRO* 5.3 2.5 - - + -
1335J LEU* 4.2 22.0 - - + -
1343J ALA 2.9 19.5 + - - +
1344J VAL 2.9 3.3 + - - +
1346J ARG* 1.3 75.3 - - - +
1348J LEU* 1.3 80.4 + - + +
1350J ASP* 3.4 4.4 + - + +
1351J GLU* 2.9 58.8 + - + +
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Residues in contact with LEU1348 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262J LEU* 5.3 17.3 - - + +
1265J ALA* 6.3 0.7 - - + -
1332J PRO* 4.1 29.6 - - + -
1344J VAL* 2.9 41.7 + - + +
1345J GLU 3.8 2.5 - - - +
1347J TYR* 1.3 83.0 - - + +
1349J VAL* 1.3 65.4 + - - +
1351J GLU* 3.1 5.8 + - - +
1352J ILE* 3.0 34.6 + - + +
1372J VAL* 4.0 28.0 - - + -
1375J MET* 4.3 21.3 - - - -
1376J LEU* 5.5 0.7 - - + -
1421J LEU* 4.3 9.4 - - + -
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Residues in contact with VAL1349 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192J LEU* 5.4 2.0 - - + -
1345J GLU* 3.0 23.3 + - + +
1346J ARG* 4.0 3.8 - - - +
1348J LEU* 1.3 76.6 - - - +
1350J ASP* 1.3 60.7 + - - +
1351J GLU 3.3 0.2 + - - -
1352J ILE* 3.8 1.4 - - - +
1353J GLN* 2.9 32.5 + - + +
1365J ASP* 4.5 28.9 - - + +
1368J ILE* 3.8 22.0 - - + -
1369J GLU* 4.1 20.0 - - + +
1372J VAL* 3.6 25.1 - - + -
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Residues in contact with ASP1350 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135J ARG* 4.8 16.1 + - - -
1346J ARG* 2.9 24.6 + - + +
1347J TYR* 3.9 5.2 - - + +
1349J VAL* 1.3 79.5 - - - +
1351J GLU* 1.3 59.4 + - + +
1353J GLN* 3.8 4.7 - - - +
1354J LYS* 2.9 40.8 + - - +
1357J ARG* 5.1 5.2 + - - +
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Residues in contact with GLU1351 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258J ARG* 3.2 31.0 + - - +
1262J LEU* 3.6 20.9 - - + -
1347J TYR* 2.9 46.4 + - + +
1348J LEU 3.7 1.6 - - - +
1350J ASP* 1.3 77.5 - - + +
1352J ILE* 1.3 66.2 + - - +
1354J LYS* 3.0 31.3 + - - +
1355J VAL* 3.0 27.9 + - - +
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Residues in contact with ILE1352 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259J VAL* 4.3 3.4 - - + -
1262J LEU* 3.6 25.6 - - + -
1263J PHE* 3.5 44.9 - - + +
1348J LEU* 3.0 22.3 + - + +
1349J VAL 3.8 2.9 - - - +
1351J GLU* 1.3 77.3 - - - +
1353J GLN* 1.3 57.5 + - - +
1355J VAL* 3.2 3.9 + - - +
1356J TYR* 3.0 57.3 + - + -
1368J ILE* 3.6 31.0 - - + -
1372J VAL* 4.8 5.6 - - + -
1375J MET* 5.5 1.3 - - + -
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Residues in contact with GLN1353 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142J SER* 3.8 3.0 + - - -
1349J VAL* 2.9 19.3 + - + +
1350J ASP* 4.1 3.8 - - - +
1352J ILE* 1.3 74.3 - - - +
1354J LYS* 1.3 60.0 + - - +
1356J TYR* 3.9 7.5 - - - +
1357J ARG* 2.9 80.3 + - - +
1361J VAL 4.6 0.2 - - - +
1363J LEU* 2.8 50.2 + - - +
1365J ASP* 2.9 26.5 + - - +
1368J ILE* 3.6 15.4 - - + +
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Residues in contact with LYS1354 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350J ASP* 2.9 31.1 + - - +
1351J GLU* 3.0 40.7 + - - +
1353J GLN* 1.3 76.2 - - - +
1355J VAL* 1.3 66.5 + - + +
1357J ARG* 3.9 3.6 - - - +
1358J ALA* 2.9 28.5 + - + +
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Residues in contact with VAL1355 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1236J LEU* 3.6 21.1 - - + -
1253J THR* 5.0 5.6 - - + -
1254J GLN* 4.8 3.6 - - + -
1255J GLY* 3.5 31.4 - - - +
1258J ARG* 3.6 33.4 - - + +
1259J VAL* 3.7 9.2 - - + -
1351J GLU* 3.0 15.8 + - - +
1352J ILE* 3.7 6.1 - - - +
1354J LYS* 1.3 78.5 - - + +
1356J TYR* 1.3 63.9 + - - +
1358J ALA* 3.2 8.1 + - - +
1359J GLN* 2.9 25.7 + - + +
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Residues in contact with TYR1356 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094J LEU* 4.7 4.3 - - - +
1229J ILE* 3.3 33.6 + - + +
1232J PRO* 3.5 35.0 - - + -
1233J GLY* 4.8 5.9 + - - -
1236J LEU* 4.6 16.2 - - + +
1256J LEU* 5.2 0.5 - - - +
1259J VAL* 3.8 26.3 - - + +
1352J ILE* 3.0 49.5 + - + +
1353J GLN* 3.9 13.9 - - - +
1355J VAL* 1.3 77.0 - - - +
1357J ARG* 1.3 57.9 + - - +
1359J GLN* 2.9 23.6 + - + +
1360J GLY 3.1 8.3 + - - -
1361J VAL* 3.1 21.5 + - + +
1363J LEU* 3.7 20.4 - - + -
1368J ILE* 5.2 0.2 - - + -
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Residues in contact with ARG1357 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124J GLN* 5.6 2.0 + - - -
1135J ARG* 3.1 33.0 - - - +
1139J ASP* 3.2 31.8 + - - +
1142J SER* 3.2 16.9 + - - -
1350J ASP* 5.1 7.7 + - - +
1353J GLN* 2.9 70.8 + - - +
1354J LYS* 4.2 3.3 - - - +
1356J TYR* 1.3 74.0 - - - +
1358J ALA* 1.3 61.5 + - - +
1360J GLY* 3.0 13.6 + - - +
1361J VAL 3.8 12.1 + - - +
1362J LYS* 5.6 5.2 - - + -
1365J ASP* 3.3 13.7 + - - -
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Residues in contact with ALA1358 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253J THR* 4.6 16.6 - - + +
1354J LYS* 2.9 23.5 + - + +
1355J VAL* 3.3 8.5 - - - +
1356J TYR 3.1 0.2 - - - -
1357J ARG* 1.3 76.9 - - - +
1359J GLN* 1.3 60.7 + - - +
1360J GLY* 3.0 1.4 + - - -
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Residues in contact with GLN1359 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1235J GLN* 4.5 9.8 - - - +
1236J LEU* 3.6 25.7 - - + +
1237J THR 3.2 37.3 + - - +
1238J MET* 3.2 49.2 - - + +
1253J THR* 4.0 13.7 - - + +
1255J GLY* 4.1 4.8 - - - -
1355J VAL* 2.9 18.0 + - + +
1356J TYR* 2.9 11.6 + - + +
1358J ALA* 1.3 75.4 - - - +
1360J GLY* 1.3 60.4 + - - +
1361J VAL* 4.4 8.5 - - + +
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Residues in contact with GLY1360 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1357J ARG 3.0 15.8 + - - -
1358J ALA 3.0 2.3 + - - -
1359J GLN* 1.3 80.8 - - - +
1361J VAL* 1.3 62.8 + - - +
1362J LYS 4.2 0.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il